Hi Mark,
the atom types in .top file is opls_???, but the atom types(or "name")
in [bondtypes] in ffoplsaabon.itp file is C, H, CT, C_3, etc.
So we still need to look up ffoplsaanb.itp to link these two "atom type"
(or "name"), right?
thanks
Qiang
Mark Abraham wrote:
friendli wrote:
So to obtain the parameters(e.g. bonds) in topology file,
1, read bond atoms in .top (e.g. 1 2)
2, find atom types of the bond atoms in .top (e.g. oplsaa_235,
oplsaa_236)
3, find atom names of the above atom types in ffoplsaanb.itp (e.g.
C, O)
4, check parameters in ffoplsaabon.itp
Is that right?
3 is irrelevant. Otherwise, you're on track. The general idea is that
indices in [bonds] look up the atom indices in [atoms] to get the atom
types which are looked up in [bondtypes] to get the parameters which
are then applied to the bonds.
why it comes to such complex in GMX?
I think it's about as simple as it can be to do all the jobs it needs
to do. You need a central repository of parameters. You need a list of
bonds, and a way to map bonded atoms to parameters. You need a
mechanism that can span multiple force field designs.
Mark
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